Azzmer Azzar Abdul Hamid

International Islamic University Malaysia | iium · Department of Biotechnology

Being commonly found at crime scenes, fingerprints are crucial for human identification, attributable to their uniqueness, persistence and systematic classification of ridge patterns. In addition to latent fingerprints being invisible to the naked eye, the escalating trends of disposing forensic evidence bearing such prints in watery bodies would f...

Agarwood is a fragrant resinous wood that has been widely used in traditional medicines, incense and perfume. Formation of agarwood in branches and trunks of certain genera including Aquilaria and Gyrinops is due to activation of defence mechanism that causes by natural phenomena or microbial infection. The main fragrant compounds of agarwood are s...

The multidrug resistance phenomenon presents a major threat to the pharmaceutical industry. This resistance is a common occurrence in several diseases and is mediated by multidrug transporters that actively pump substances out of the cell and away from their target regions. The most well-known multidrug transporter is the P-glycoprotein transporter...

The quick response of contaminants from various sources and the extensive deterioration of rivers’ water quality may harm our biodiversity, aquatic creatures, and environment. The depletion of this river water quality can be caused by both natural and manmade factors and this condition will jeopardize its use for many human uses and may harm the re...

Introduction: One of the potential antihypertensive mechanisms include angiotensin converting enzyme (ACE) inhibition. So far, there is no in-depth study on the ACE inhibition activity of S. polyanthum, an ethnomedicinal plant used in treating hypertension. Thus, we aimed to study the ACE inhibition activity of S. polyanthum leaves by evaluating it...

Efficacy of a β-1,4-glucosidase from Trichoderma harzianum T12 (ThBglT12) in disrupting the cell wall of the phytopathogenic fungus M. phaseolina (Macrophomina phaseolina) was studied, as the underlying molecular mechanisms of cell wall recognition remains elusive. In this study, the binding location identified by a consensus of residues predicted...

The data presented here is the liquid chromatography and mass spectrometry (LC-MS) profile of phytochemical compounds in the aqueous extract of Syzygium polyanthum (Wight) Walp. leaves. This plant is consumed raw and sometimes added to local dishes of people in Southeast Asia countries. Most importantly, it has ethnomedicinal values mainly in treat...

This is the first structural model of L-haloacid dehalogenase (DehLBHS1) isolated from alkalotolerant Bacillus megaterium BHS1, which has been known to degrading halogenated environmental contaminants. The study suggested five important key amino acid residues of DehLBHS1, namely Arg40, Phe59, Asn118, Asn176 and Trp178 important for catalysis and m...

This study explored the potential of Acacia mangium to remediate arsenic present in mine wastes and to determine the remediation mechanism of this plant for removing arsenic. A preliminary test using soil spiked with various arsenic concentrations showed that Acacia mangium was able to survive on arsenic-contaminated soil with concentrations up to...

Increased scientific interest has led to the rise in biotechnological uses of halophilic and halotolerant microbes for hypersaline wastewater bioremediation. Hence, this study performed molecular docking, molecular dynamic (MD) simulations, and validation by Molecular Mechanic Poisson-Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from...

Stress hormone is the number one adversary to the general health in human all over the world. In the presence of stress, cortisol, a glucocorticoid hormone synthesized by the stimulation of adrenal cortex will be secreted. Cortisol has immunosuppressive and anti-inflammatory effects, increases heart rate and blood pressure, and represses growth, an...

Purpose: Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi Gölü (Blue Lake, Turkey), can grow on minimal medium containing 2,2-dichloropropionic acid. We characterized this bacterium at the genomic level. Methods: The HiSeq platform was used to carry out genome sequencing, de novo assembly, and scaffolding with...

The 16S rRNA amplicon sequencing technique is a key aspect of studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. This work aimed to assess the structure of the uncultured bacterial communities from two locations in Lake Tuz in Turkey to provide information on their roles in the lake ecosy...

An acid, 2,2-dichloropropionic acid (2,2-DCP) is an active ingredient in herbicide (Dalapon®). Using 2,2-DCP as a model substrate, an alkalotolerant bacterium was successfully isolated from the Blue Lake, Turkey. This bacterium is a potential bioremediation agent of recalcitrant xenobiotic halogenated compounds. This stu-dy aimed to prove the effic...

Dengue fever, which is a disease caused by the dengue virus (DENV), is a major unsolved issue in many tropical and sub-tropical regions of the world. The absence of treatment that effectively prevent further viral propagation inside the human’s body resulted in a high number of deaths globally each year. Thus, novel anti-dengue therapies are requir...

Aptamers are oligonucleotides and peptides around 15–100 bases in length and are suitable as detection probes or as therapeutics molecules. There are growing interests in the aptamer screening approach through computational simulation methods. DNA and RNA modelling lacks of validation on their predicted 3D structures due to less number of validatio...

Extensive deterioration of water quality caused by the intensive land use activities in rivers and rapid response of pollutants from different sources may harm the aquatic organisms, humans, and the environment. The water quality of the Balok River is believed has been deteriorated by anthropogenic impact as a result of the industrial activities in...

Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary str...

Considering the significant evidential values of fingerprints in underwater criminal investigations and the need to visualise them using a user- and environmentally-friendly reagent, development of a novel, rapid and relatively greener nanobio-based reagent (NBR) deemed beneficial. Lipase from the commercial Candida rugosa immobilised onto acid-fun...

Literature have shown that oil palm leaves (OPL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by the Trichoderma species. However, mechanism of β-glucosidase and xylanase selectivity to degrade lignin, hemicellulose and cellulose in OPL for NC production remains relatively vague. The stud...

We previously reported on a mutant lipase KV1 (Mut-LipKV1) from Acinetobacter haemolyticus which optimal pH was raised from 8.0 to 11.0 after triple substitutions of surface aspartic acid (Asp) with lysine (Lys). Herein, this study further examined the Mut-LipKV1 by molecular docking, molecular dynamics (MD) simulations and molecular mechanics-Pois...

The ability of Streptococcus pneumoniae to induce infections relies on its virulence factor machinery. A previous CRISPR interference (CRISPRi) study had identified 254 essential proteins that may be responsible towards the pathogenicity of S. pneumoniae serotype 2 strain D39. However, 39 of them were functionally and structurally uncharacterized....

Fruit bromelain is a proteolytic enzyme harbouring cysteine catalytic residue found abundantly in pineapple fruit. The expression of cysteine proteases is usually regulated during fruit ripening. In the present study, we aimed to study the expression and proteolytic activity level of fruit bromelain during the ripening stage of A. comosus cultivar...

The ability of Streptococcus pneumoniae to induce infection relies on its virulence factor machinery. A previous study has identified essential proteins that might be responsible towards the pathogenicity of S. pneumoniae serotype 2 strain D39. However, 39 of them were yet functionally and structurally uncharacterized. Thus, by using in silico appr...

Alkaline-stable lipases are highly valuable biocatalysts that catalyze reactions under highly basic conditions. Herein, computational predictions of lipase from Acinetobacter haemolyticus and its mutant, Mut-LipKV1 was performed to identify functionally relevant mutations that enhance pH performance under increasing basicity. Mut-LipKV1 was constru...

Fungi of the Trichoderma species are valued industrial enzymes in support of the ‘zero-waste’ technology to convert agro-industrial biomass into valuable products, i.e. nanocellulose (NC). In this study, an in silico approach using substrate docking and molecular dynamic simulation was used to predict the order of which the multilayers of cellulosi...

Communicated by Ramaswamy H. Sarma.

Aptamer has been long studied as a substitute of antibodies for many purposes. However, due to the exceeded length of the aptamers obtained in vitro , difficulties arise in its manipulation during its molecular conjugation on the matrix surfaces. Current study focuses on computational improvement for aptamers screening of hepatitis B surface antige...

Dehalogenase E (DehE) is a non-stereospecific enzyme produced by the soil bacterium, Rhizobium sp. RC1. Till now, the catalytic mechanism of DehE remains unclear although several literature concerning its structure and function are available. Since DehE is non-stereospecific, the enzyme was hypothesized to follow a ‘direct attack mechanism’ for the...

Enzyme is important as biocatalyst for industrial and biotechnological applications. Cold active enzymes have showed many advantages compare to mesophilic enzymes. Their cold active and thermolabile characteristics have shown potential benefits in many industries. In silico characterization of hydrolytic enzymes originated from polar and tropical r...

Aptamers are oligonucleotides and peptides with short and medium length around 15-100 nucleotides or amino acids and a molecule of interests due to its specific binding affinities to the vast array of target molecules such as ions, complex proteins and antigens up to cellular surface and cell organelles. Aptamers shows high potential of application...

Molecular docking was done to assess the binding affinity of 6-paradol (6PRD), Zingerone (ZGR) and Zerumbone (ZRB) ligand-ERα complex in comparison to Hydroxytamoxifen (HTMX). Docking results showed that Glu353 and Arg394 active residues forms hydrogen bonding with 6PRD and ZGR. Glu353, Leu387 and Arg394 were the three identical residues found to f...

Simulation and computational analysis of 6-gingerol and 6-shogaol is done to evaluate their binding affinity against ERα. Active site prediction was done using Computed Atlas of Surface Topography of Proteins (CASTp) to determine the binding pocket of ERα. Molecular docking and molecular dynamics (MD) simulation were done to assess the binding affi...

Cysteine proteases in pineapple (Ananas comosus) plants are phytotherapeutical agents that demonstrate anti-edematous, anti-inflammatory, anti-thrombotic and fibrinolytic activities. Bromelain has been identified as an active component and as a major protease of A. comosus. Bromelain has gained wide acceptance and compliance as a phytotherapeutical...

Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (...

Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles...

E. coli DH5α harbouring pET28a+ plasmid vector was lysed by alkaline lysis and the clarified plasmid solutions were subjected to ultrafiltration experiments using two types of ultrafiltration membrane; i.e., cellulose generated (Ultracel) and polyethersulfome PES (Biomax). Transmembrane pressures (TMP) through vacuum suction of 0.1 to 0.7 bar were...

Aims: This study presents the first structural model and proposed the identity of four important key amino acid residues, Asp13, Arg51, Ser131 and Asp207 for the stereospecific haloalkanoic acid dehalogenase from Rhizobium sp. RC1. Methodology and results: The enzyme was built using a homology modeling technique; the structure of crystallized L-DEX...

Synthetic haloalkanoic acid (HA) is one of the synthetics compounds that can be found as active ingredients in herbicides. These compounds are known to pollute our agriculture land due to their toxicity, thus may cause serious environmental and health problems. Biological process such as microbial dehalogenation degrades the harmful compounds and p...

Lactic acid bacteria (LAB) confer many advantages to humans and animals and they provide natural protection against bacterial pathogens such as Salmonella typhymurium and Eschericia coli. LAB strains have been isolated from various animal sources but from this research LAB were isolated from quail’s (Coturnix coturnix Japonica) intestine. About 12...

Salts 2,2-dichloropropionic acid or dalapon are well-known active components of herbicides regurlarly found as contaminants in the water system and soil. Nonetheless, continuous consumption of water contaminated with such substances may pose significant threat to living organism especially mammals. Fortunately, these toxic subtances may be eliminat...

Enzymes are macromolecular biological catalysis that is important to speed up reaction. Enzymes can be found naturally from the microorganism such as bacteria, fungi and yeast which may not be genetically modified. In this perspectives, resorting to bioremediation to clean-up such environment may prove feasible and beneficial as microorganisms effe...

Enzymes are macromolecular biological catalysis that is important to speed up reaction. Enzymes can be found naturally from the microorganism such as bacteria, fungi and yeast which may not be genetically modified. In this perspectives, resorting to bioremediation to clean-up such environment may prove feasible and beneficial as microorganisms effe...

Introduction: DehE or non-stereospecific dehalogenase from Rhizobium sp. RC1 catalyzes the hydrolytic dehalogenation of both isomers of D,L-2-haloacids to produce an inverted configuration of 2-hydroxyl acid. The enzymatic degradation for the removal of halides from haloacid substance has been highlighted since the enzyme itself is a potential cand...

Sponges (Porifera) harbour diverse microorganisms which can be the potential source for microbial enzymes such as lipase. In this study, moderately halophilic lipase producing bacteria were isolated from sponges tissues collected near Balok, at Pahang coastal water. Out of 70 isolates that grew on tributyrin agar plate, only 7 isolates had produced...

Synthetic haloalkanoic acids often applied as active components in herbicides are toxic to the environment and harmful to the living organisms. These compounds are widely released to the environment due to their routine use by agricultural activities. In recent years, accumulation of haloalkanoic acids was emerged in marine environment. In this stu...

The non-stereospecific α-haloalkanoic acid dehalogenase E (DehE) degrades many halogenated compounds but is ineffective against β-halogenated compounds such as 3-chloropropionic acid (3CP). Using molecular dynamics (MD) simulations and site-directed mutagenesis we show here that introducing the mutation S188V into DehE improves substrate specificit...

Halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. Notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the D-specific dehalogenase fro...

Halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. Notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the D-specific dehalogenase...

Many environmental pollutions are caused by the abundance of xenobiotic compounds in nature. For instance, halogenated compounds released from chemical industries were proven to be toxic and recalcitrant in the environment. However, haloalkanoic acid dehalogenases can catalyse the removal of halides from organic haloacids and thus have gained inter...

Arthrobacter sp. strains D2 and D3 and Labrys sp. strain D1 capable of degrading 20 mM monochloroacetic acid (MCA) were isolated from soil contaminated with herbicides and pesticides. All three isolates were able to grow on MCA as the sole source of carbon and energy with concomitant chloride ion release in the growth medium (19 mM). Strains D2 and...

The non-stereospecific α-haloalkanoic acid dehalogenase DehE from Rhizobium sp. RC1 catalyzes the removal of the halide from α-haloalkanoic acid D,L-stereoisomers and, by doing so, converts them into hydroxyalkanoic acid L,D-stereoisomers, respectively. DehE has been extensively studied to determine its potential to act as a bioremediation agent, b...

Aims: The present study aimed at molecular identification of putative Cof-like hydrolase associated with dehalogenase gene from a bacterium that was isolated from a contaminated sea-side area in the Philippines. The bacterium was subjected to 16S rRNA gene sequence analysis for identity of the genus and species. Methodology and results: Based on ba...

Haloalkanoic acid dehalogenases remove halides from organic haloacids and have potential as bioremediation agents. DehE from Rhizobium sp. RC1, DehI from Pseudomonas putida PP3 and D,L-DEX 113 from Pseudomonas sp. 113 are non-stereospecific dehalogenases that invert the configurations of D-and L-carbons bound to a halogen. The kinetics of DehE has...

Halogenated compounds are widely used in agriculture and industries and have been associated with environmental pollution. Degradation of 3-chloropropionate (3CP) by microorganism has been established and this enzyme could only remove halogen atom at the -position of 3-carbon alkanoic acids. Pseudomonas sp. B6P was originally isolated from paddy fi...

Haloacetic acids (HAAs) are group of chemicals formed due to disinfection by products that can be detected during chlorination and chloramination of processed drinking water. In this study, Bacillus sp. strain TW1 identified by morphological/biochemical and PCR-amplified 16S rRNA gene was isolated from Kuala Terengganu water treatment and distribut...

A phylogenetic analysis of an unknown strain AZZ2 isolated from volcanic area Gunung Sibayak Indonesia was performed. Their phylogenetic relationships were analysed using MEGA4 software<SUP>®</SUP> to ascertain its evolutionary distance by reconstructing a phylogenetic tree of these organisms. The evolutionary history and bootstrap consensus tree w...

Pseudomonas sp. strain S3 was isolated from Paddy (rice) field agricultural area. This organism, which can utilize a halogenated compound of D,L-2-Chloropropionic acid as sole carbon and energy source, catalyses the hydrolytic dehalogenation of both D- and L- isomers of 2-Chloropropionic acid. Identification of Pseudomonas sp. S3 is still ambiguous...